Why is mercury a liquid at room temperature, but iron isn't a liquid until the temperature is raised to about 2000 degrees Celsius? Why is water a liquid at room temperature, but (luckily) nitrogen and oxygen don't become liquids until the temperature is much, much lower?

The answer is -- it depends on the forces between the atoms or molecules.

How can we model a solid/liquid/gas ?

We start with knowing something about the interaction of just two particles. We need to know how the forces between the two particles depend on the distance between the particles. One common feature about the interactions between two particles is that they repel at short distances, attract each other for moderate distances and are close to zero for large distances.

How does the simulation work ? The force on an individual particle is the sum of the forces from all the other particles. This sum is easy to do on a computer. Then, if we know the force, we can predict how the particle will move -- at least for the next little bit of time. Why only for a little bit of time? Because all the other particles are moving too, and so the force on a particle changes. We do this same process for each particle and that way predict how the whole group of particles will act.

How is temperature included ? Temperature is basically a measure of how fast the particles are moving. When we start the simulation, we can choose the initial velocity for each particle. For high temperatures we use larger velocities, while for low temperatures we use smaller velocities.

Obviously if the molecules are moving faster (higher temperature) it will be harder for the attractive forces between the molecules to hold them close to each other. So at very high temperatures, we have a gas where the molecules fly around independently of each other. At low temperatures (slow velocities) the attractive forces keep the molecules close together and we have a liquid or a solid.

Molecular Dynamics Applications Simulations of small numbers of atoms or molecules are now used in many fields. For example molecular dynamics is used to look at protein folding, the design of new drugs, and the growth of thin films.